RNA sequencing:Article Title: Impact of eIF2α phosphorylation on the translational landscape of mouse embryonic stem cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data mESC Ribo-Seq and RNA-Seq data This Study GEO: GSE248729 mESC MS data This Study Tables S3 and S4 Experimental models: Cell lines Mouse: mESCs (derived from eIF2aS51A/+ mice) Scheuner et al., 200120 PMID: 11430820 Human: 293T ATCC Cat#CRL-3216 Mouse: N2A ATCC Cat#CCL-131 Experimental Models: Organisms/Strains Mouse: eIF2a S51A/+: B6; 129-Eif2s1tm1Rjk/J Scheuner et al., 200120 PMID: 11430820 Oligonucleotides Primers for RT-qPCR and PCR. see Table S5 This Paper Table S5 Scramble siRNA Dharmacon Reagents Cat#D-001810-10-05 siRNA targeting ATF4 Dharmacon Reagents Cat#L-042737-01-0005 Recombinant DNA psPAX2 Didier Trono Lab: Packaging and Envelope Plasmids (unpublished) Addgene plasmid # 12260 pMD2.G Didier Trono Lab: Packaging and Envelope Plasmids (unpublished) Addgene plasmid # 12259 pLKO.1-puro Empty Vector Control Plasmid DNA Sigma-Aldrich SHC001 PLKO.1-shATF4 Plasmid (TRCN0000301646) McGill Platform for Cellular Perturbation (MPCP) N/A Software and algorithms Cutadapt 3.4 Martin, 201181 http://code.google.com/p/cutadapt/ Bowtie 1.3.0 Langmead et al., 200982 http://bowtie.cbcb.umd.edu Mouse Gencode version M25 comprehensive transcriptome Gencode https://ftp.ebi.ac.uk/pub/databases/ gencode/Gencode_mouse/release_M25/ UMI-Tools 1.0.1 Smith et al., 201783 https://GitHub.com/CGATOxford/UMI- tools Trips-Viz Kiniry et al., 202184 https://trips.ucc.ie/ R package deltaTE (DTE) version 1.34.0 Chothani et al., 201939 https://github.com/SGDDNB/translational_ regulation Python package Vienna RNA version 2.1.9 Lorenz et al., 201185 http://www.tbi.univie.ac.at/RNA Comet-base software pipeline Eng et al., 201386; Huttlin et al., 201087 https://comet-ms.sourceforge.net/https:// phosphomouse.hms.harvard.edu/ Linear Discriminant Analysis Elias and Gygi, 200788; 201089 PMID: 17327847, 20013364 AScore Beausoleil et al., 200690 http://ascore.med.harvard.edu/ Fastx v0.0.13.2 Cold Spring Harbor Laboratory http://hannonlab.cshl.edu/fastx_toolkit/ .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data mESC Ribo-Seq and RNA-Seq data This Study GEO: GSE248729 mESC MS data This Study Tables S3 and S4 Experimental models: Cell lines Mouse: mESCs (derived from eIF2aS51A/+ mice) Scheuner et al., 200120 PMID: 11430820 Human: 293T ATCC Cat#CRL-3216 Mouse: N2A ATCC Cat#CCL-131 Experimental Models: Organisms/Strains Mouse: eIF2a S51A/+: B6; 129-Eif2s1tm1Rjk/J Scheuner et al., 200120 PMID: 11430820 Oligonucleotides Primers for RT-qPCR and PCR. see Table S5 This Paper Table S5 Scramble siRNA Dharmacon Reagents Cat#D-001810-10-05 siRNA targeting ATF4 Dharmacon Reagents Cat#L-042737-01-0005 Recombinant DNA psPAX2 Didier Trono Lab: Packaging and Envelope Plasmids (unpublished) Addgene plasmid # 12260 pMD2.G Didier Trono Lab: Packaging and Envelope Plasmids (unpublished) Addgene plasmid # 12259 pLKO.1-puro Empty Vector Control Plasmid DNA Sigma-Aldrich SHC001 PLKO.1-shATF4 Plasmid (TRCN0000301646) McGill Platform for Cellular Perturbation (MPCP) N/A Software and algorithms Cutadapt 3.4 Martin, 201181 http://code.google.com/p/cutadapt/ Bowtie 1.3.0 Langmead et al., 200982 http://bowtie.cbcb.umd.edu Mouse Gencode version M25 comprehensive transcriptome Gencode https://ftp.ebi.ac.uk/pub/databases/ gencode/Gencode_mouse/release_M25/ UMI-Tools 1.0.1 Smith et al., 201783 https://GitHub.com/CGATOxford/UMI- tools Trips-Viz Kiniry et al., 202184 https://trips.ucc.ie/ R package deltaTE (DTE) version 1.34.0 Chothani et al., 201939 https://github.com/SGDDNB/translational_ regulation Python package Vienna RNA version 2.1.9 Lorenz et al., 201185 http://www.tbi.univie.ac.at/RNA Comet-base software pipeline Eng et al., 201386; Huttlin et al., 201087 https://comet-ms.sourceforge.net/https:// phosphomouse.hms.harvard.edu/ Linear Discriminant Analysis Elias and Gygi, 200788; 201089 PMID: 17327847, 20013364 AScore Beausoleil et al., 200690 http://ascore.med.harvard.edu/ Fastx v0.0.13.2 Cold Spring Harbor Laboratory http://hannonlab.cshl.edu/fastx_toolkit/
Derivative Assay:Article Title: Impact of eIF2α phosphorylation on the translational landscape of mouse embryonic stem cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data mESC Ribo-Seq and RNA-Seq data This Study GEO: GSE248729 mESC MS data This Study Tables S3 and S4 Experimental models: Cell lines Mouse: mESCs (derived from eIF2aS51A/+ mice) Scheuner et al., 200120 PMID: 11430820 Human: 293T ATCC Cat#CRL-3216 Mouse: N2A ATCC Cat#CCL-131 Experimental Models: Organisms/Strains Mouse: eIF2a S51A/+: B6; 129-Eif2s1tm1Rjk/J Scheuner et al., 200120 PMID: 11430820 Oligonucleotides Primers for RT-qPCR and PCR. see Table S5 This Paper Table S5 Scramble siRNA Dharmacon Reagents Cat#D-001810-10-05 siRNA targeting ATF4 Dharmacon Reagents Cat#L-042737-01-0005 Recombinant DNA psPAX2 Didier Trono Lab: Packaging and Envelope Plasmids (unpublished) Addgene plasmid # 12260 pMD2.G Didier Trono Lab: Packaging and Envelope Plasmids (unpublished) Addgene plasmid # 12259 pLKO.1-puro Empty Vector Control Plasmid DNA Sigma-Aldrich SHC001 PLKO.1-shATF4 Plasmid (TRCN0000301646) McGill Platform for Cellular Perturbation (MPCP) N/A Software and algorithms Cutadapt 3.4 Martin, 201181 http://code.google.com/p/cutadapt/ Bowtie 1.3.0 Langmead et al., 200982 http://bowtie.cbcb.umd.edu Mouse Gencode version M25 comprehensive transcriptome Gencode https://ftp.ebi.ac.uk/pub/databases/ gencode/Gencode_mouse/release_M25/ UMI-Tools 1.0.1 Smith et al., 201783 https://GitHub.com/CGATOxford/UMI- tools Trips-Viz Kiniry et al., 202184 https://trips.ucc.ie/ R package deltaTE (DTE) version 1.34.0 Chothani et al., 201939 https://github.com/SGDDNB/translational_ regulation Python package Vienna RNA version 2.1.9 Lorenz et al., 201185 http://www.tbi.univie.ac.at/RNA Comet-base software pipeline Eng et al., 201386; Huttlin et al., 201087 https://comet-ms.sourceforge.net/https:// phosphomouse.hms.harvard.edu/ Linear Discriminant Analysis Elias and Gygi, 200788; 201089 PMID: 17327847, 20013364 AScore Beausoleil et al., 200690 http://ascore.med.harvard.edu/ Fastx v0.0.13.2 Cold Spring Harbor Laboratory http://hannonlab.cshl.edu/fastx_toolkit/ .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data mESC Ribo-Seq and RNA-Seq data This Study GEO: GSE248729 mESC MS data This Study Tables S3 and S4 Experimental models: Cell lines Mouse: mESCs (derived from eIF2aS51A/+ mice) Scheuner et al., 200120 PMID: 11430820 Human: 293T ATCC Cat#CRL-3216 Mouse: N2A ATCC Cat#CCL-131 Experimental Models: Organisms/Strains Mouse: eIF2a S51A/+: B6; 129-Eif2s1tm1Rjk/J Scheuner et al., 200120 PMID: 11430820 Oligonucleotides Primers for RT-qPCR and PCR. see Table S5 This Paper Table S5 Scramble siRNA Dharmacon Reagents Cat#D-001810-10-05 siRNA targeting ATF4 Dharmacon Reagents Cat#L-042737-01-0005 Recombinant DNA psPAX2 Didier Trono Lab: Packaging and Envelope Plasmids (unpublished) Addgene plasmid # 12260 pMD2.G Didier Trono Lab: Packaging and Envelope Plasmids (unpublished) Addgene plasmid # 12259 pLKO.1-puro Empty Vector Control Plasmid DNA Sigma-Aldrich SHC001 PLKO.1-shATF4 Plasmid (TRCN0000301646) McGill Platform for Cellular Perturbation (MPCP) N/A Software and algorithms Cutadapt 3.4 Martin, 201181 http://code.google.com/p/cutadapt/ Bowtie 1.3.0 Langmead et al., 200982 http://bowtie.cbcb.umd.edu Mouse Gencode version M25 comprehensive transcriptome Gencode https://ftp.ebi.ac.uk/pub/databases/ gencode/Gencode_mouse/release_M25/ UMI-Tools 1.0.1 Smith et al., 201783 https://GitHub.com/CGATOxford/UMI- tools Trips-Viz Kiniry et al., 202184 https://trips.ucc.ie/ R package deltaTE (DTE) version 1.34.0 Chothani et al., 201939 https://github.com/SGDDNB/translational_ regulation Python package Vienna RNA version 2.1.9 Lorenz et al., 201185 http://www.tbi.univie.ac.at/RNA Comet-base software pipeline Eng et al., 201386; Huttlin et al., 201087 https://comet-ms.sourceforge.net/https:// phosphomouse.hms.harvard.edu/ Linear Discriminant Analysis Elias and Gygi, 200788; 201089 PMID: 17327847, 20013364 AScore Beausoleil et al., 200690 http://ascore.med.harvard.edu/ Fastx v0.0.13.2 Cold Spring Harbor Laboratory http://hannonlab.cshl.edu/fastx_toolkit/
Quantitative RT-PCR:Article Title: Impact of eIF2α phosphorylation on the translational landscape of mouse embryonic stem cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data mESC Ribo-Seq and RNA-Seq data This Study GEO: GSE248729 mESC MS data This Study Tables S3 and S4 Experimental models: Cell lines Mouse: mESCs (derived from eIF2aS51A/+ mice) Scheuner et al., 200120 PMID: 11430820 Human: 293T ATCC Cat#CRL-3216 Mouse: N2A ATCC Cat#CCL-131 Experimental Models: Organisms/Strains Mouse: eIF2a S51A/+: B6; 129-Eif2s1tm1Rjk/J Scheuner et al., 200120 PMID: 11430820 Oligonucleotides Primers for RT-qPCR and PCR. see Table S5 This Paper Table S5 Scramble siRNA Dharmacon Reagents Cat#D-001810-10-05 siRNA targeting ATF4 Dharmacon Reagents Cat#L-042737-01-0005 Recombinant DNA psPAX2 Didier Trono Lab: Packaging and Envelope Plasmids (unpublished) Addgene plasmid # 12260 pMD2.G Didier Trono Lab: Packaging and Envelope Plasmids (unpublished) Addgene plasmid # 12259 pLKO.1-puro Empty Vector Control Plasmid DNA Sigma-Aldrich SHC001 PLKO.1-shATF4 Plasmid (TRCN0000301646) McGill Platform for Cellular Perturbation (MPCP) N/A Software and algorithms Cutadapt 3.4 Martin, 201181 http://code.google.com/p/cutadapt/ Bowtie 1.3.0 Langmead et al., 200982 http://bowtie.cbcb.umd.edu Mouse Gencode version M25 comprehensive transcriptome Gencode https://ftp.ebi.ac.uk/pub/databases/ gencode/Gencode_mouse/release_M25/ UMI-Tools 1.0.1 Smith et al., 201783 https://GitHub.com/CGATOxford/UMI- tools Trips-Viz Kiniry et al., 202184 https://trips.ucc.ie/ R package deltaTE (DTE) version 1.34.0 Chothani et al., 201939 https://github.com/SGDDNB/translational_ regulation Python package Vienna RNA version 2.1.9 Lorenz et al., 201185 http://www.tbi.univie.ac.at/RNA Comet-base software pipeline Eng et al., 201386; Huttlin et al., 201087 https://comet-ms.sourceforge.net/https:// phosphomouse.hms.harvard.edu/ Linear Discriminant Analysis Elias and Gygi, 200788; 201089 PMID: 17327847, 20013364 AScore Beausoleil et al., 200690 http://ascore.med.harvard.edu/ Fastx v0.0.13.2 Cold Spring Harbor Laboratory http://hannonlab.cshl.edu/fastx_toolkit/ .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data mESC Ribo-Seq and RNA-Seq data This Study GEO: GSE248729 mESC MS data This Study Tables S3 and S4 Experimental models: Cell lines Mouse: mESCs (derived from eIF2aS51A/+ mice) Scheuner et al., 200120 PMID: 11430820 Human: 293T ATCC Cat#CRL-3216 Mouse: N2A ATCC Cat#CCL-131 Experimental Models: Organisms/Strains Mouse: eIF2a S51A/+: B6; 129-Eif2s1tm1Rjk/J Scheuner et al., 200120 PMID: 11430820 Oligonucleotides Primers for RT-qPCR and PCR. see Table S5 This Paper Table S5 Scramble siRNA Dharmacon Reagents Cat#D-001810-10-05 siRNA targeting ATF4 Dharmacon Reagents Cat#L-042737-01-0005 Recombinant DNA psPAX2 Didier Trono Lab: Packaging and Envelope Plasmids (unpublished) Addgene plasmid # 12260 pMD2.G Didier Trono Lab: Packaging and Envelope Plasmids (unpublished) Addgene plasmid # 12259 pLKO.1-puro Empty Vector Control Plasmid DNA Sigma-Aldrich SHC001 PLKO.1-shATF4 Plasmid (TRCN0000301646) McGill Platform for Cellular Perturbation (MPCP) N/A Software and algorithms Cutadapt 3.4 Martin, 201181 http://code.google.com/p/cutadapt/ Bowtie 1.3.0 Langmead et al., 200982 http://bowtie.cbcb.umd.edu Mouse Gencode version M25 comprehensive transcriptome Gencode https://ftp.ebi.ac.uk/pub/databases/ gencode/Gencode_mouse/release_M25/ UMI-Tools 1.0.1 Smith et al., 201783 https://GitHub.com/CGATOxford/UMI- tools Trips-Viz Kiniry et al., 202184 https://trips.ucc.ie/ R package deltaTE (DTE) version 1.34.0 Chothani et al., 201939 https://github.com/SGDDNB/translational_ regulation Python package Vienna RNA version 2.1.9 Lorenz et al., 201185 http://www.tbi.univie.ac.at/RNA Comet-base software pipeline Eng et al., 201386; Huttlin et al., 201087 https://comet-ms.sourceforge.net/https:// phosphomouse.hms.harvard.edu/ Linear Discriminant Analysis Elias and Gygi, 200788; 201089 PMID: 17327847, 20013364 AScore Beausoleil et al., 200690 http://ascore.med.harvard.edu/ Fastx v0.0.13.2 Cold Spring Harbor Laboratory http://hannonlab.cshl.edu/fastx_toolkit/
Polymerase Chain Reaction:Article Title: Impact of eIF2α phosphorylation on the translational landscape of mouse embryonic stem cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data mESC Ribo-Seq and RNA-Seq data This Study GEO: GSE248729 mESC MS data This Study Tables S3 and S4 Experimental models: Cell lines Mouse: mESCs (derived from eIF2aS51A/+ mice) Scheuner et al., 200120 PMID: 11430820 Human: 293T ATCC Cat#CRL-3216 Mouse: N2A ATCC Cat#CCL-131 Experimental Models: Organisms/Strains Mouse: eIF2a S51A/+: B6; 129-Eif2s1tm1Rjk/J Scheuner et al., 200120 PMID: 11430820 Oligonucleotides Primers for RT-qPCR and PCR. see Table S5 This Paper Table S5 Scramble siRNA Dharmacon Reagents Cat#D-001810-10-05 siRNA targeting ATF4 Dharmacon Reagents Cat#L-042737-01-0005 Recombinant DNA psPAX2 Didier Trono Lab: Packaging and Envelope Plasmids (unpublished) Addgene plasmid # 12260 pMD2.G Didier Trono Lab: Packaging and Envelope Plasmids (unpublished) Addgene plasmid # 12259 pLKO.1-puro Empty Vector Control Plasmid DNA Sigma-Aldrich SHC001 PLKO.1-shATF4 Plasmid (TRCN0000301646) McGill Platform for Cellular Perturbation (MPCP) N/A Software and algorithms Cutadapt 3.4 Martin, 201181 http://code.google.com/p/cutadapt/ Bowtie 1.3.0 Langmead et al., 200982 http://bowtie.cbcb.umd.edu Mouse Gencode version M25 comprehensive transcriptome Gencode https://ftp.ebi.ac.uk/pub/databases/ gencode/Gencode_mouse/release_M25/ UMI-Tools 1.0.1 Smith et al., 201783 https://GitHub.com/CGATOxford/UMI- tools Trips-Viz Kiniry et al., 202184 https://trips.ucc.ie/ R package deltaTE (DTE) version 1.34.0 Chothani et al., 201939 https://github.com/SGDDNB/translational_ regulation Python package Vienna RNA version 2.1.9 Lorenz et al., 201185 http://www.tbi.univie.ac.at/RNA Comet-base software pipeline Eng et al., 201386; Huttlin et al., 201087 https://comet-ms.sourceforge.net/https:// phosphomouse.hms.harvard.edu/ Linear Discriminant Analysis Elias and Gygi, 200788; 201089 PMID: 17327847, 20013364 AScore Beausoleil et al., 200690 http://ascore.med.harvard.edu/ Fastx v0.0.13.2 Cold Spring Harbor Laboratory http://hannonlab.cshl.edu/fastx_toolkit/ .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data mESC Ribo-Seq and RNA-Seq data This Study GEO: GSE248729 mESC MS data This Study Tables S3 and S4 Experimental models: Cell lines Mouse: mESCs (derived from eIF2aS51A/+ mice) Scheuner et al., 200120 PMID: 11430820 Human: 293T ATCC Cat#CRL-3216 Mouse: N2A ATCC Cat#CCL-131 Experimental Models: Organisms/Strains Mouse: eIF2a S51A/+: B6; 129-Eif2s1tm1Rjk/J Scheuner et al., 200120 PMID: 11430820 Oligonucleotides Primers for RT-qPCR and PCR. see Table S5 This Paper Table S5 Scramble siRNA Dharmacon Reagents Cat#D-001810-10-05 siRNA targeting ATF4 Dharmacon Reagents Cat#L-042737-01-0005 Recombinant DNA psPAX2 Didier Trono Lab: Packaging and Envelope Plasmids (unpublished) Addgene plasmid # 12260 pMD2.G Didier Trono Lab: Packaging and Envelope Plasmids (unpublished) Addgene plasmid # 12259 pLKO.1-puro Empty Vector Control Plasmid DNA Sigma-Aldrich SHC001 PLKO.1-shATF4 Plasmid (TRCN0000301646) McGill Platform for Cellular Perturbation (MPCP) N/A Software and algorithms Cutadapt 3.4 Martin, 201181 http://code.google.com/p/cutadapt/ Bowtie 1.3.0 Langmead et al., 200982 http://bowtie.cbcb.umd.edu Mouse Gencode version M25 comprehensive transcriptome Gencode https://ftp.ebi.ac.uk/pub/databases/ gencode/Gencode_mouse/release_M25/ UMI-Tools 1.0.1 Smith et al., 201783 https://GitHub.com/CGATOxford/UMI- tools Trips-Viz Kiniry et al., 202184 https://trips.ucc.ie/ R package deltaTE (DTE) version 1.34.0 Chothani et al., 201939 https://github.com/SGDDNB/translational_ regulation Python package Vienna RNA version 2.1.9 Lorenz et al., 201185 http://www.tbi.univie.ac.at/RNA Comet-base software pipeline Eng et al., 201386; Huttlin et al., 201087 https://comet-ms.sourceforge.net/https:// phosphomouse.hms.harvard.edu/ Linear Discriminant Analysis Elias and Gygi, 200788; 201089 PMID: 17327847, 20013364 AScore Beausoleil et al., 200690 http://ascore.med.harvard.edu/ Fastx v0.0.13.2 Cold Spring Harbor Laboratory http://hannonlab.cshl.edu/fastx_toolkit/
Recombinant:Article Title: Impact of eIF2α phosphorylation on the translational landscape of mouse embryonic stem cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data mESC Ribo-Seq and RNA-Seq data This Study GEO: GSE248729 mESC MS data This Study Tables S3 and S4 Experimental models: Cell lines Mouse: mESCs (derived from eIF2aS51A/+ mice) Scheuner et al., 200120 PMID: 11430820 Human: 293T ATCC Cat#CRL-3216 Mouse: N2A ATCC Cat#CCL-131 Experimental Models: Organisms/Strains Mouse: eIF2a S51A/+: B6; 129-Eif2s1tm1Rjk/J Scheuner et al., 200120 PMID: 11430820 Oligonucleotides Primers for RT-qPCR and PCR. see Table S5 This Paper Table S5 Scramble siRNA Dharmacon Reagents Cat#D-001810-10-05 siRNA targeting ATF4 Dharmacon Reagents Cat#L-042737-01-0005 Recombinant DNA psPAX2 Didier Trono Lab: Packaging and Envelope Plasmids (unpublished) Addgene plasmid # 12260 pMD2.G Didier Trono Lab: Packaging and Envelope Plasmids (unpublished) Addgene plasmid # 12259 pLKO.1-puro Empty Vector Control Plasmid DNA Sigma-Aldrich SHC001 PLKO.1-shATF4 Plasmid (TRCN0000301646) McGill Platform for Cellular Perturbation (MPCP) N/A Software and algorithms Cutadapt 3.4 Martin, 201181 http://code.google.com/p/cutadapt/ Bowtie 1.3.0 Langmead et al., 200982 http://bowtie.cbcb.umd.edu Mouse Gencode version M25 comprehensive transcriptome Gencode https://ftp.ebi.ac.uk/pub/databases/ gencode/Gencode_mouse/release_M25/ UMI-Tools 1.0.1 Smith et al., 201783 https://GitHub.com/CGATOxford/UMI- tools Trips-Viz Kiniry et al., 202184 https://trips.ucc.ie/ R package deltaTE (DTE) version 1.34.0 Chothani et al., 201939 https://github.com/SGDDNB/translational_ regulation Python package Vienna RNA version 2.1.9 Lorenz et al., 201185 http://www.tbi.univie.ac.at/RNA Comet-base software pipeline Eng et al., 201386; Huttlin et al., 201087 https://comet-ms.sourceforge.net/https:// phosphomouse.hms.harvard.edu/ Linear Discriminant Analysis Elias and Gygi, 200788; 201089 PMID: 17327847, 20013364 AScore Beausoleil et al., 200690 http://ascore.med.harvard.edu/ Fastx v0.0.13.2 Cold Spring Harbor Laboratory http://hannonlab.cshl.edu/fastx_toolkit/ .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data mESC Ribo-Seq and RNA-Seq data This Study GEO: GSE248729 mESC MS data This Study Tables S3 and S4 Experimental models: Cell lines Mouse: mESCs (derived from eIF2aS51A/+ mice) Scheuner et al., 200120 PMID: 11430820 Human: 293T ATCC Cat#CRL-3216 Mouse: N2A ATCC Cat#CCL-131 Experimental Models: Organisms/Strains Mouse: eIF2a S51A/+: B6; 129-Eif2s1tm1Rjk/J Scheuner et al., 200120 PMID: 11430820 Oligonucleotides Primers for RT-qPCR and PCR. see Table S5 This Paper Table S5 Scramble siRNA Dharmacon Reagents Cat#D-001810-10-05 siRNA targeting ATF4 Dharmacon Reagents Cat#L-042737-01-0005 Recombinant DNA psPAX2 Didier Trono Lab: Packaging and Envelope Plasmids (unpublished) Addgene plasmid # 12260 pMD2.G Didier Trono Lab: Packaging and Envelope Plasmids (unpublished) Addgene plasmid # 12259 pLKO.1-puro Empty Vector Control Plasmid DNA Sigma-Aldrich SHC001 PLKO.1-shATF4 Plasmid (TRCN0000301646) McGill Platform for Cellular Perturbation (MPCP) N/A Software and algorithms Cutadapt 3.4 Martin, 201181 http://code.google.com/p/cutadapt/ Bowtie 1.3.0 Langmead et al., 200982 http://bowtie.cbcb.umd.edu Mouse Gencode version M25 comprehensive transcriptome Gencode https://ftp.ebi.ac.uk/pub/databases/ gencode/Gencode_mouse/release_M25/ UMI-Tools 1.0.1 Smith et al., 201783 https://GitHub.com/CGATOxford/UMI- tools Trips-Viz Kiniry et al., 202184 https://trips.ucc.ie/ R package deltaTE (DTE) version 1.34.0 Chothani et al., 201939 https://github.com/SGDDNB/translational_ regulation Python package Vienna RNA version 2.1.9 Lorenz et al., 201185 http://www.tbi.univie.ac.at/RNA Comet-base software pipeline Eng et al., 201386; Huttlin et al., 201087 https://comet-ms.sourceforge.net/https:// phosphomouse.hms.harvard.edu/ Linear Discriminant Analysis Elias and Gygi, 200788; 201089 PMID: 17327847, 20013364 AScore Beausoleil et al., 200690 http://ascore.med.harvard.edu/ Fastx v0.0.13.2 Cold Spring Harbor Laboratory http://hannonlab.cshl.edu/fastx_toolkit/
Article Title: Crosstalk between epitranscriptomic and epigenomic modifications and its implication in human diseases
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rabbit polyclonal anti-m6A ABclonal Cat# A17924; RRID: AB_2770239 Chemicals, peptides, and recombinant proteins Dulbecco’s modified eagles’s medium VivaCell Cat# C3113-0500 fetal bovine serum Gibco Cat# 10270-106 RPMI-1640 VivaCell Cat# C3010-0500 Puromycin Gibco Cat# A11138-03 1M Tris-HCl 7.5 Invitrogen Cat# 15567-027 IGEPAL CA-630 MP Biomedicals Cat# 198596 Murine RNase Inhibitor Vazyme Cat# R301 5M NaCl Invitrogen Cat# AM9760G TRIzon reagent CWBIO Cat# CW0580S Critical commercial assays Lipofectamine 3000 reagent Thermo Fisher Scientific Cat# L3000015 FastPure Cell/Tissue Total RNA Isolation Kit Vazyme Cat# RC101-01 One Step TB Green PrimeScrip RT-PCR Kit Takara Cat# RR066 Universal Genomic DNA Kit CWBIO Cat# CW2298M EZ DNA Methylation Kit Zymo Research Cat# D5002 ChamQ Universal SYBR qPCR Master Mix Vazyme Cat# Q711 Dynabeads mRNA DIRECT purification kit Thermo Fisher Scientific Cat# 61011 NEBNext Magnesium RNA Fragmentation Module NEB Cat# E6150S RNA Clean & Concentrator-5 kit Zymo Research Cat# R1016 Direct-zol RNA Microprep Kit Zymo Research Cat# R2060 Deposited data m6A-QTL summary statistics for brain, lung, muscle, and heart tissues from the eGTEx project Xiong et al.21 https://compbio.mit.edu/m6AQTLs/m6A. .. QTL.Xiong.etal/SumStat/ haQTL summary statistics for brain, lung, muscle, and heart tissues from the eGTEx project Hou et al.50 https://zenodo.org/records/7992724 mQTL summary statistics for lung and muscle tissues from the eGTEx project Oliva et al.51 https://gtexportal.org/home/datasets Code used in this study This manuscript https://doi.org/10.5281/zenodo.11481934 Experimental models: Cell lines Human: A549 ATCC(CRL-185) N/A Human: HEK293T ATCC(CRL-11268) N/A Oligonucleotides Oligonucleotides used in this study for experimental validation Table S13 N/A Recombinant DNA Plasmid: pLKO.1 Moffat et al.92 Addgene Plasmid # 10878 Plasmid: psPAX2 Trono Lab Packaging and Envelope Plasmids (unpublished) Addgene Plasmid # 12260 Plasmid: pMD2.G Trono Lab Packaging and Envelope Plasmids (unpublished) Addgene Plasmid # 12259 (Continued on next page) Cell Genomics 4, 100605, August 14, 2024 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms TwoSampleMR v0.5.6 Hemani et al.93 https://mrcieu.github.io/TwoSampleMR/ SMR Zhu et al.53 https://yanglab.westlake.edu.cn/software/ smr/ bedtools v2.31.0 Quinlan et al.94 https://bedtools.readthedocs.io/en/latest/ coloc v5.2.2 Giambartolomei et al.54 https://chr1swallace.github.io/coloc/ S-LDSC v1.0.1 Bulik-Sullivan et al.82 https://github.com/bulik/ldsc moloc v0.1.0 Giambartolomei et al.73 https://github.com/clagiamba/moloc Other Protein A/G Magnetic Beads Selleck Cat# B23201 Article ll OPEN ACCESS
Article Title: Crosstalk between epitranscriptomic and epigenomic modifications and its implication in human diseases.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rabbit polyclonal anti-m6A ABclonal Cat# A17924; RRID: AB_2770239 Chemicals, peptides, and recombinant proteins Dulbecco’s modified eagles’s medium VivaCell Cat# C3113-0500 fetal bovine serum Gibco Cat# 10270-106 RPMI-1640 VivaCell Cat# C3010-0500 Puromycin Gibco Cat# A11138-03 1M Tris-HCl 7.5 Invitrogen Cat# 15567-027 IGEPAL CA-630 MP Biomedicals Cat# 198596 Murine RNase Inhibitor Vazyme Cat# R301 5M NaCl Invitrogen Cat# AM9760G TRIzon reagent CWBIO Cat# CW0580S Critical commercial assays Lipofectamine 3000 reagent Thermo Fisher Scientific Cat# L3000015 FastPure Cell/Tissue Total RNA Isolation Kit Vazyme Cat# RC101-01 One Step TB Green PrimeScrip RT-PCR Kit Takara Cat# RR066 Universal Genomic DNA Kit CWBIO Cat# CW2298M EZ DNA Methylation Kit Zymo Research Cat# D5002 ChamQ Universal SYBR qPCR Master Mix Vazyme Cat# Q711 Dynabeads mRNA DIRECT purification kit Thermo Fisher Scientific Cat# 61011 NEBNext Magnesium RNA Fragmentation Module NEB Cat# E6150S RNA Clean & Concentrator-5 kit Zymo Research Cat# R1016 Direct-zol RNA Microprep Kit Zymo Research Cat# R2060 Deposited data m6A-QTL summary statistics for brain, lung, muscle, and heart tissues from the eGTEx project Xiong et al.21 https://compbio.mit.edu/m6AQTLs/m6A. .. QTL.Xiong.etal/SumStat/ haQTL summary statistics for brain, lung, muscle, and heart tissues from the eGTEx project Hou et al.50 https://zenodo.org/records/7992724 mQTL summary statistics for lung and muscle tissues from the eGTEx project Oliva et al.51 https://gtexportal.org/home/datasets Code used in this study This manuscript https://doi.org/10.5281/zenodo.11481934 Experimental models: Cell lines Human: A549 ATCC(CRL-185) N/A Human: HEK293T ATCC(CRL-11268) N/A Oligonucleotides Oligonucleotides used in this study for experimental validation Table S13 N/A Recombinant DNA Plasmid: pLKO.1 Moffat et al.92 Addgene Plasmid # 10878 Plasmid: psPAX2 Trono Lab Packaging and Envelope Plasmids (unpublished) Addgene Plasmid # 12260 Plasmid: pMD2.G Trono Lab Packaging and Envelope Plasmids (unpublished) Addgene Plasmid # 12259 (Continued on next page) Cell Genomics 4, 100605, August 14, 2024 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms TwoSampleMR v0.5.6 Hemani et al.93 https://mrcieu.github.io/TwoSampleMR/ SMR Zhu et al.53 https://yanglab.westlake.edu.cn/software/ smr/ bedtools v2.31.0 Quinlan et al.94 https://bedtools.readthedocs.io/en/latest/ coloc v5.2.2 Giambartolomei et al.54 https://chr1swallace.github.io/coloc/ S-LDSC v1.0.1 Bulik-Sullivan et al.82 https://github.com/bulik/ldsc moloc v0.1.0 Giambartolomei et al.73 https://github.com/clagiamba/moloc Other Protein A/G Magnetic Beads Selleck Cat# B23201
Plasmid Preparation:Article Title: Impact of eIF2α phosphorylation on the translational landscape of mouse embryonic stem cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data mESC Ribo-Seq and RNA-Seq data This Study GEO: GSE248729 mESC MS data This Study Tables S3 and S4 Experimental models: Cell lines Mouse: mESCs (derived from eIF2aS51A/+ mice) Scheuner et al., 200120 PMID: 11430820 Human: 293T ATCC Cat#CRL-3216 Mouse: N2A ATCC Cat#CCL-131 Experimental Models: Organisms/Strains Mouse: eIF2a S51A/+: B6; 129-Eif2s1tm1Rjk/J Scheuner et al., 200120 PMID: 11430820 Oligonucleotides Primers for RT-qPCR and PCR. see Table S5 This Paper Table S5 Scramble siRNA Dharmacon Reagents Cat#D-001810-10-05 siRNA targeting ATF4 Dharmacon Reagents Cat#L-042737-01-0005 Recombinant DNA psPAX2 Didier Trono Lab: Packaging and Envelope Plasmids (unpublished) Addgene plasmid # 12260 pMD2.G Didier Trono Lab: Packaging and Envelope Plasmids (unpublished) Addgene plasmid # 12259 pLKO.1-puro Empty Vector Control Plasmid DNA Sigma-Aldrich SHC001 PLKO.1-shATF4 Plasmid (TRCN0000301646) McGill Platform for Cellular Perturbation (MPCP) N/A Software and algorithms Cutadapt 3.4 Martin, 201181 http://code.google.com/p/cutadapt/ Bowtie 1.3.0 Langmead et al., 200982 http://bowtie.cbcb.umd.edu Mouse Gencode version M25 comprehensive transcriptome Gencode https://ftp.ebi.ac.uk/pub/databases/ gencode/Gencode_mouse/release_M25/ UMI-Tools 1.0.1 Smith et al., 201783 https://GitHub.com/CGATOxford/UMI- tools Trips-Viz Kiniry et al., 202184 https://trips.ucc.ie/ R package deltaTE (DTE) version 1.34.0 Chothani et al., 201939 https://github.com/SGDDNB/translational_ regulation Python package Vienna RNA version 2.1.9 Lorenz et al., 201185 http://www.tbi.univie.ac.at/RNA Comet-base software pipeline Eng et al., 201386; Huttlin et al., 201087 https://comet-ms.sourceforge.net/https:// phosphomouse.hms.harvard.edu/ Linear Discriminant Analysis Elias and Gygi, 200788; 201089 PMID: 17327847, 20013364 AScore Beausoleil et al., 200690 http://ascore.med.harvard.edu/ Fastx v0.0.13.2 Cold Spring Harbor Laboratory http://hannonlab.cshl.edu/fastx_toolkit/ .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data mESC Ribo-Seq and RNA-Seq data This Study GEO: GSE248729 mESC MS data This Study Tables S3 and S4 Experimental models: Cell lines Mouse: mESCs (derived from eIF2aS51A/+ mice) Scheuner et al., 200120 PMID: 11430820 Human: 293T ATCC Cat#CRL-3216 Mouse: N2A ATCC Cat#CCL-131 Experimental Models: Organisms/Strains Mouse: eIF2a S51A/+: B6; 129-Eif2s1tm1Rjk/J Scheuner et al., 200120 PMID: 11430820 Oligonucleotides Primers for RT-qPCR and PCR. see Table S5 This Paper Table S5 Scramble siRNA Dharmacon Reagents Cat#D-001810-10-05 siRNA targeting ATF4 Dharmacon Reagents Cat#L-042737-01-0005 Recombinant DNA psPAX2 Didier Trono Lab: Packaging and Envelope Plasmids (unpublished) Addgene plasmid # 12260 pMD2.G Didier Trono Lab: Packaging and Envelope Plasmids (unpublished) Addgene plasmid # 12259 pLKO.1-puro Empty Vector Control Plasmid DNA Sigma-Aldrich SHC001 PLKO.1-shATF4 Plasmid (TRCN0000301646) McGill Platform for Cellular Perturbation (MPCP) N/A Software and algorithms Cutadapt 3.4 Martin, 201181 http://code.google.com/p/cutadapt/ Bowtie 1.3.0 Langmead et al., 200982 http://bowtie.cbcb.umd.edu Mouse Gencode version M25 comprehensive transcriptome Gencode https://ftp.ebi.ac.uk/pub/databases/ gencode/Gencode_mouse/release_M25/ UMI-Tools 1.0.1 Smith et al., 201783 https://GitHub.com/CGATOxford/UMI- tools Trips-Viz Kiniry et al., 202184 https://trips.ucc.ie/ R package deltaTE (DTE) version 1.34.0 Chothani et al., 201939 https://github.com/SGDDNB/translational_ regulation Python package Vienna RNA version 2.1.9 Lorenz et al., 201185 http://www.tbi.univie.ac.at/RNA Comet-base software pipeline Eng et al., 201386; Huttlin et al., 201087 https://comet-ms.sourceforge.net/https:// phosphomouse.hms.harvard.edu/ Linear Discriminant Analysis Elias and Gygi, 200788; 201089 PMID: 17327847, 20013364 AScore Beausoleil et al., 200690 http://ascore.med.harvard.edu/ Fastx v0.0.13.2 Cold Spring Harbor Laboratory http://hannonlab.cshl.edu/fastx_toolkit/
Article Title: Crosstalk between epitranscriptomic and epigenomic modifications and its implication in human diseases
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rabbit polyclonal anti-m6A ABclonal Cat# A17924; RRID: AB_2770239 Chemicals, peptides, and recombinant proteins Dulbecco’s modified eagles’s medium VivaCell Cat# C3113-0500 fetal bovine serum Gibco Cat# 10270-106 RPMI-1640 VivaCell Cat# C3010-0500 Puromycin Gibco Cat# A11138-03 1M Tris-HCl 7.5 Invitrogen Cat# 15567-027 IGEPAL CA-630 MP Biomedicals Cat# 198596 Murine RNase Inhibitor Vazyme Cat# R301 5M NaCl Invitrogen Cat# AM9760G TRIzon reagent CWBIO Cat# CW0580S Critical commercial assays Lipofectamine 3000 reagent Thermo Fisher Scientific Cat# L3000015 FastPure Cell/Tissue Total RNA Isolation Kit Vazyme Cat# RC101-01 One Step TB Green PrimeScrip RT-PCR Kit Takara Cat# RR066 Universal Genomic DNA Kit CWBIO Cat# CW2298M EZ DNA Methylation Kit Zymo Research Cat# D5002 ChamQ Universal SYBR qPCR Master Mix Vazyme Cat# Q711 Dynabeads mRNA DIRECT purification kit Thermo Fisher Scientific Cat# 61011 NEBNext Magnesium RNA Fragmentation Module NEB Cat# E6150S RNA Clean & Concentrator-5 kit Zymo Research Cat# R1016 Direct-zol RNA Microprep Kit Zymo Research Cat# R2060 Deposited data m6A-QTL summary statistics for brain, lung, muscle, and heart tissues from the eGTEx project Xiong et al.21 https://compbio.mit.edu/m6AQTLs/m6A. .. QTL.Xiong.etal/SumStat/ haQTL summary statistics for brain, lung, muscle, and heart tissues from the eGTEx project Hou et al.50 https://zenodo.org/records/7992724 mQTL summary statistics for lung and muscle tissues from the eGTEx project Oliva et al.51 https://gtexportal.org/home/datasets Code used in this study This manuscript https://doi.org/10.5281/zenodo.11481934 Experimental models: Cell lines Human: A549 ATCC(CRL-185) N/A Human: HEK293T ATCC(CRL-11268) N/A Oligonucleotides Oligonucleotides used in this study for experimental validation Table S13 N/A Recombinant DNA Plasmid: pLKO.1 Moffat et al.92 Addgene Plasmid # 10878 Plasmid: psPAX2 Trono Lab Packaging and Envelope Plasmids (unpublished) Addgene Plasmid # 12260 Plasmid: pMD2.G Trono Lab Packaging and Envelope Plasmids (unpublished) Addgene Plasmid # 12259 (Continued on next page) Cell Genomics 4, 100605, August 14, 2024 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms TwoSampleMR v0.5.6 Hemani et al.93 https://mrcieu.github.io/TwoSampleMR/ SMR Zhu et al.53 https://yanglab.westlake.edu.cn/software/ smr/ bedtools v2.31.0 Quinlan et al.94 https://bedtools.readthedocs.io/en/latest/ coloc v5.2.2 Giambartolomei et al.54 https://chr1swallace.github.io/coloc/ S-LDSC v1.0.1 Bulik-Sullivan et al.82 https://github.com/bulik/ldsc moloc v0.1.0 Giambartolomei et al.73 https://github.com/clagiamba/moloc Other Protein A/G Magnetic Beads Selleck Cat# B23201 Article ll OPEN ACCESS
Article Title: Crosstalk between epitranscriptomic and epigenomic modifications and its implication in human diseases.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rabbit polyclonal anti-m6A ABclonal Cat# A17924; RRID: AB_2770239 Chemicals, peptides, and recombinant proteins Dulbecco’s modified eagles’s medium VivaCell Cat# C3113-0500 fetal bovine serum Gibco Cat# 10270-106 RPMI-1640 VivaCell Cat# C3010-0500 Puromycin Gibco Cat# A11138-03 1M Tris-HCl 7.5 Invitrogen Cat# 15567-027 IGEPAL CA-630 MP Biomedicals Cat# 198596 Murine RNase Inhibitor Vazyme Cat# R301 5M NaCl Invitrogen Cat# AM9760G TRIzon reagent CWBIO Cat# CW0580S Critical commercial assays Lipofectamine 3000 reagent Thermo Fisher Scientific Cat# L3000015 FastPure Cell/Tissue Total RNA Isolation Kit Vazyme Cat# RC101-01 One Step TB Green PrimeScrip RT-PCR Kit Takara Cat# RR066 Universal Genomic DNA Kit CWBIO Cat# CW2298M EZ DNA Methylation Kit Zymo Research Cat# D5002 ChamQ Universal SYBR qPCR Master Mix Vazyme Cat# Q711 Dynabeads mRNA DIRECT purification kit Thermo Fisher Scientific Cat# 61011 NEBNext Magnesium RNA Fragmentation Module NEB Cat# E6150S RNA Clean & Concentrator-5 kit Zymo Research Cat# R1016 Direct-zol RNA Microprep Kit Zymo Research Cat# R2060 Deposited data m6A-QTL summary statistics for brain, lung, muscle, and heart tissues from the eGTEx project Xiong et al.21 https://compbio.mit.edu/m6AQTLs/m6A. .. QTL.Xiong.etal/SumStat/ haQTL summary statistics for brain, lung, muscle, and heart tissues from the eGTEx project Hou et al.50 https://zenodo.org/records/7992724 mQTL summary statistics for lung and muscle tissues from the eGTEx project Oliva et al.51 https://gtexportal.org/home/datasets Code used in this study This manuscript https://doi.org/10.5281/zenodo.11481934 Experimental models: Cell lines Human: A549 ATCC(CRL-185) N/A Human: HEK293T ATCC(CRL-11268) N/A Oligonucleotides Oligonucleotides used in this study for experimental validation Table S13 N/A Recombinant DNA Plasmid: pLKO.1 Moffat et al.92 Addgene Plasmid # 10878 Plasmid: psPAX2 Trono Lab Packaging and Envelope Plasmids (unpublished) Addgene Plasmid # 12260 Plasmid: pMD2.G Trono Lab Packaging and Envelope Plasmids (unpublished) Addgene Plasmid # 12259 (Continued on next page) Cell Genomics 4, 100605, August 14, 2024 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms TwoSampleMR v0.5.6 Hemani et al.93 https://mrcieu.github.io/TwoSampleMR/ SMR Zhu et al.53 https://yanglab.westlake.edu.cn/software/ smr/ bedtools v2.31.0 Quinlan et al.94 https://bedtools.readthedocs.io/en/latest/ coloc v5.2.2 Giambartolomei et al.54 https://chr1swallace.github.io/coloc/ S-LDSC v1.0.1 Bulik-Sullivan et al.82 https://github.com/bulik/ldsc moloc v0.1.0 Giambartolomei et al.73 https://github.com/clagiamba/moloc Other Protein A/G Magnetic Beads Selleck Cat# B23201
Control:Article Title: Impact of eIF2α phosphorylation on the translational landscape of mouse embryonic stem cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data mESC Ribo-Seq and RNA-Seq data This Study GEO: GSE248729 mESC MS data This Study Tables S3 and S4 Experimental models: Cell lines Mouse: mESCs (derived from eIF2aS51A/+ mice) Scheuner et al., 200120 PMID: 11430820 Human: 293T ATCC Cat#CRL-3216 Mouse: N2A ATCC Cat#CCL-131 Experimental Models: Organisms/Strains Mouse: eIF2a S51A/+: B6; 129-Eif2s1tm1Rjk/J Scheuner et al., 200120 PMID: 11430820 Oligonucleotides Primers for RT-qPCR and PCR. see Table S5 This Paper Table S5 Scramble siRNA Dharmacon Reagents Cat#D-001810-10-05 siRNA targeting ATF4 Dharmacon Reagents Cat#L-042737-01-0005 Recombinant DNA psPAX2 Didier Trono Lab: Packaging and Envelope Plasmids (unpublished) Addgene plasmid # 12260 pMD2.G Didier Trono Lab: Packaging and Envelope Plasmids (unpublished) Addgene plasmid # 12259 pLKO.1-puro Empty Vector Control Plasmid DNA Sigma-Aldrich SHC001 PLKO.1-shATF4 Plasmid (TRCN0000301646) McGill Platform for Cellular Perturbation (MPCP) N/A Software and algorithms Cutadapt 3.4 Martin, 201181 http://code.google.com/p/cutadapt/ Bowtie 1.3.0 Langmead et al., 200982 http://bowtie.cbcb.umd.edu Mouse Gencode version M25 comprehensive transcriptome Gencode https://ftp.ebi.ac.uk/pub/databases/ gencode/Gencode_mouse/release_M25/ UMI-Tools 1.0.1 Smith et al., 201783 https://GitHub.com/CGATOxford/UMI- tools Trips-Viz Kiniry et al., 202184 https://trips.ucc.ie/ R package deltaTE (DTE) version 1.34.0 Chothani et al., 201939 https://github.com/SGDDNB/translational_ regulation Python package Vienna RNA version 2.1.9 Lorenz et al., 201185 http://www.tbi.univie.ac.at/RNA Comet-base software pipeline Eng et al., 201386; Huttlin et al., 201087 https://comet-ms.sourceforge.net/https:// phosphomouse.hms.harvard.edu/ Linear Discriminant Analysis Elias and Gygi, 200788; 201089 PMID: 17327847, 20013364 AScore Beausoleil et al., 200690 http://ascore.med.harvard.edu/ Fastx v0.0.13.2 Cold Spring Harbor Laboratory http://hannonlab.cshl.edu/fastx_toolkit/ .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data mESC Ribo-Seq and RNA-Seq data This Study GEO: GSE248729 mESC MS data This Study Tables S3 and S4 Experimental models: Cell lines Mouse: mESCs (derived from eIF2aS51A/+ mice) Scheuner et al., 200120 PMID: 11430820 Human: 293T ATCC Cat#CRL-3216 Mouse: N2A ATCC Cat#CCL-131 Experimental Models: Organisms/Strains Mouse: eIF2a S51A/+: B6; 129-Eif2s1tm1Rjk/J Scheuner et al., 200120 PMID: 11430820 Oligonucleotides Primers for RT-qPCR and PCR. see Table S5 This Paper Table S5 Scramble siRNA Dharmacon Reagents Cat#D-001810-10-05 siRNA targeting ATF4 Dharmacon Reagents Cat#L-042737-01-0005 Recombinant DNA psPAX2 Didier Trono Lab: Packaging and Envelope Plasmids (unpublished) Addgene plasmid # 12260 pMD2.G Didier Trono Lab: Packaging and Envelope Plasmids (unpublished) Addgene plasmid # 12259 pLKO.1-puro Empty Vector Control Plasmid DNA Sigma-Aldrich SHC001 PLKO.1-shATF4 Plasmid (TRCN0000301646) McGill Platform for Cellular Perturbation (MPCP) N/A Software and algorithms Cutadapt 3.4 Martin, 201181 http://code.google.com/p/cutadapt/ Bowtie 1.3.0 Langmead et al., 200982 http://bowtie.cbcb.umd.edu Mouse Gencode version M25 comprehensive transcriptome Gencode https://ftp.ebi.ac.uk/pub/databases/ gencode/Gencode_mouse/release_M25/ UMI-Tools 1.0.1 Smith et al., 201783 https://GitHub.com/CGATOxford/UMI- tools Trips-Viz Kiniry et al., 202184 https://trips.ucc.ie/ R package deltaTE (DTE) version 1.34.0 Chothani et al., 201939 https://github.com/SGDDNB/translational_ regulation Python package Vienna RNA version 2.1.9 Lorenz et al., 201185 http://www.tbi.univie.ac.at/RNA Comet-base software pipeline Eng et al., 201386; Huttlin et al., 201087 https://comet-ms.sourceforge.net/https:// phosphomouse.hms.harvard.edu/ Linear Discriminant Analysis Elias and Gygi, 200788; 201089 PMID: 17327847, 20013364 AScore Beausoleil et al., 200690 http://ascore.med.harvard.edu/ Fastx v0.0.13.2 Cold Spring Harbor Laboratory http://hannonlab.cshl.edu/fastx_toolkit/
Software:Article Title: Impact of eIF2α phosphorylation on the translational landscape of mouse embryonic stem cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data mESC Ribo-Seq and RNA-Seq data This Study GEO: GSE248729 mESC MS data This Study Tables S3 and S4 Experimental models: Cell lines Mouse: mESCs (derived from eIF2aS51A/+ mice) Scheuner et al., 200120 PMID: 11430820 Human: 293T ATCC Cat#CRL-3216 Mouse: N2A ATCC Cat#CCL-131 Experimental Models: Organisms/Strains Mouse: eIF2a S51A/+: B6; 129-Eif2s1tm1Rjk/J Scheuner et al., 200120 PMID: 11430820 Oligonucleotides Primers for RT-qPCR and PCR. see Table S5 This Paper Table S5 Scramble siRNA Dharmacon Reagents Cat#D-001810-10-05 siRNA targeting ATF4 Dharmacon Reagents Cat#L-042737-01-0005 Recombinant DNA psPAX2 Didier Trono Lab: Packaging and Envelope Plasmids (unpublished) Addgene plasmid # 12260 pMD2.G Didier Trono Lab: Packaging and Envelope Plasmids (unpublished) Addgene plasmid # 12259 pLKO.1-puro Empty Vector Control Plasmid DNA Sigma-Aldrich SHC001 PLKO.1-shATF4 Plasmid (TRCN0000301646) McGill Platform for Cellular Perturbation (MPCP) N/A Software and algorithms Cutadapt 3.4 Martin, 201181 http://code.google.com/p/cutadapt/ Bowtie 1.3.0 Langmead et al., 200982 http://bowtie.cbcb.umd.edu Mouse Gencode version M25 comprehensive transcriptome Gencode https://ftp.ebi.ac.uk/pub/databases/ gencode/Gencode_mouse/release_M25/ UMI-Tools 1.0.1 Smith et al., 201783 https://GitHub.com/CGATOxford/UMI- tools Trips-Viz Kiniry et al., 202184 https://trips.ucc.ie/ R package deltaTE (DTE) version 1.34.0 Chothani et al., 201939 https://github.com/SGDDNB/translational_ regulation Python package Vienna RNA version 2.1.9 Lorenz et al., 201185 http://www.tbi.univie.ac.at/RNA Comet-base software pipeline Eng et al., 201386; Huttlin et al., 201087 https://comet-ms.sourceforge.net/https:// phosphomouse.hms.harvard.edu/ Linear Discriminant Analysis Elias and Gygi, 200788; 201089 PMID: 17327847, 20013364 AScore Beausoleil et al., 200690 http://ascore.med.harvard.edu/ Fastx v0.0.13.2 Cold Spring Harbor Laboratory http://hannonlab.cshl.edu/fastx_toolkit/ .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data mESC Ribo-Seq and RNA-Seq data This Study GEO: GSE248729 mESC MS data This Study Tables S3 and S4 Experimental models: Cell lines Mouse: mESCs (derived from eIF2aS51A/+ mice) Scheuner et al., 200120 PMID: 11430820 Human: 293T ATCC Cat#CRL-3216 Mouse: N2A ATCC Cat#CCL-131 Experimental Models: Organisms/Strains Mouse: eIF2a S51A/+: B6; 129-Eif2s1tm1Rjk/J Scheuner et al., 200120 PMID: 11430820 Oligonucleotides Primers for RT-qPCR and PCR. see Table S5 This Paper Table S5 Scramble siRNA Dharmacon Reagents Cat#D-001810-10-05 siRNA targeting ATF4 Dharmacon Reagents Cat#L-042737-01-0005 Recombinant DNA psPAX2 Didier Trono Lab: Packaging and Envelope Plasmids (unpublished) Addgene plasmid # 12260 pMD2.G Didier Trono Lab: Packaging and Envelope Plasmids (unpublished) Addgene plasmid # 12259 pLKO.1-puro Empty Vector Control Plasmid DNA Sigma-Aldrich SHC001 PLKO.1-shATF4 Plasmid (TRCN0000301646) McGill Platform for Cellular Perturbation (MPCP) N/A Software and algorithms Cutadapt 3.4 Martin, 201181 http://code.google.com/p/cutadapt/ Bowtie 1.3.0 Langmead et al., 200982 http://bowtie.cbcb.umd.edu Mouse Gencode version M25 comprehensive transcriptome Gencode https://ftp.ebi.ac.uk/pub/databases/ gencode/Gencode_mouse/release_M25/ UMI-Tools 1.0.1 Smith et al., 201783 https://GitHub.com/CGATOxford/UMI- tools Trips-Viz Kiniry et al., 202184 https://trips.ucc.ie/ R package deltaTE (DTE) version 1.34.0 Chothani et al., 201939 https://github.com/SGDDNB/translational_ regulation Python package Vienna RNA version 2.1.9 Lorenz et al., 201185 http://www.tbi.univie.ac.at/RNA Comet-base software pipeline Eng et al., 201386; Huttlin et al., 201087 https://comet-ms.sourceforge.net/https:// phosphomouse.hms.harvard.edu/ Linear Discriminant Analysis Elias and Gygi, 200788; 201089 PMID: 17327847, 20013364 AScore Beausoleil et al., 200690 http://ascore.med.harvard.edu/ Fastx v0.0.13.2 Cold Spring Harbor Laboratory http://hannonlab.cshl.edu/fastx_toolkit/
Biomarker Discovery:Article Title: Crosstalk between epitranscriptomic and epigenomic modifications and its implication in human diseases
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rabbit polyclonal anti-m6A ABclonal Cat# A17924; RRID: AB_2770239 Chemicals, peptides, and recombinant proteins Dulbecco’s modified eagles’s medium VivaCell Cat# C3113-0500 fetal bovine serum Gibco Cat# 10270-106 RPMI-1640 VivaCell Cat# C3010-0500 Puromycin Gibco Cat# A11138-03 1M Tris-HCl 7.5 Invitrogen Cat# 15567-027 IGEPAL CA-630 MP Biomedicals Cat# 198596 Murine RNase Inhibitor Vazyme Cat# R301 5M NaCl Invitrogen Cat# AM9760G TRIzon reagent CWBIO Cat# CW0580S Critical commercial assays Lipofectamine 3000 reagent Thermo Fisher Scientific Cat# L3000015 FastPure Cell/Tissue Total RNA Isolation Kit Vazyme Cat# RC101-01 One Step TB Green PrimeScrip RT-PCR Kit Takara Cat# RR066 Universal Genomic DNA Kit CWBIO Cat# CW2298M EZ DNA Methylation Kit Zymo Research Cat# D5002 ChamQ Universal SYBR qPCR Master Mix Vazyme Cat# Q711 Dynabeads mRNA DIRECT purification kit Thermo Fisher Scientific Cat# 61011 NEBNext Magnesium RNA Fragmentation Module NEB Cat# E6150S RNA Clean & Concentrator-5 kit Zymo Research Cat# R1016 Direct-zol RNA Microprep Kit Zymo Research Cat# R2060 Deposited data m6A-QTL summary statistics for brain, lung, muscle, and heart tissues from the eGTEx project Xiong et al.21 https://compbio.mit.edu/m6AQTLs/m6A. .. QTL.Xiong.etal/SumStat/ haQTL summary statistics for brain, lung, muscle, and heart tissues from the eGTEx project Hou et al.50 https://zenodo.org/records/7992724 mQTL summary statistics for lung and muscle tissues from the eGTEx project Oliva et al.51 https://gtexportal.org/home/datasets Code used in this study This manuscript https://doi.org/10.5281/zenodo.11481934 Experimental models: Cell lines Human: A549 ATCC(CRL-185) N/A Human: HEK293T ATCC(CRL-11268) N/A Oligonucleotides Oligonucleotides used in this study for experimental validation Table S13 N/A Recombinant DNA Plasmid: pLKO.1 Moffat et al.92 Addgene Plasmid # 10878 Plasmid: psPAX2 Trono Lab Packaging and Envelope Plasmids (unpublished) Addgene Plasmid # 12260 Plasmid: pMD2.G Trono Lab Packaging and Envelope Plasmids (unpublished) Addgene Plasmid # 12259 (Continued on next page) Cell Genomics 4, 100605, August 14, 2024 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms TwoSampleMR v0.5.6 Hemani et al.93 https://mrcieu.github.io/TwoSampleMR/ SMR Zhu et al.53 https://yanglab.westlake.edu.cn/software/ smr/ bedtools v2.31.0 Quinlan et al.94 https://bedtools.readthedocs.io/en/latest/ coloc v5.2.2 Giambartolomei et al.54 https://chr1swallace.github.io/coloc/ S-LDSC v1.0.1 Bulik-Sullivan et al.82 https://github.com/bulik/ldsc moloc v0.1.0 Giambartolomei et al.73 https://github.com/clagiamba/moloc Other Protein A/G Magnetic Beads Selleck Cat# B23201 Article ll OPEN ACCESS
Article Title: Crosstalk between epitranscriptomic and epigenomic modifications and its implication in human diseases.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rabbit polyclonal anti-m6A ABclonal Cat# A17924; RRID: AB_2770239 Chemicals, peptides, and recombinant proteins Dulbecco’s modified eagles’s medium VivaCell Cat# C3113-0500 fetal bovine serum Gibco Cat# 10270-106 RPMI-1640 VivaCell Cat# C3010-0500 Puromycin Gibco Cat# A11138-03 1M Tris-HCl 7.5 Invitrogen Cat# 15567-027 IGEPAL CA-630 MP Biomedicals Cat# 198596 Murine RNase Inhibitor Vazyme Cat# R301 5M NaCl Invitrogen Cat# AM9760G TRIzon reagent CWBIO Cat# CW0580S Critical commercial assays Lipofectamine 3000 reagent Thermo Fisher Scientific Cat# L3000015 FastPure Cell/Tissue Total RNA Isolation Kit Vazyme Cat# RC101-01 One Step TB Green PrimeScrip RT-PCR Kit Takara Cat# RR066 Universal Genomic DNA Kit CWBIO Cat# CW2298M EZ DNA Methylation Kit Zymo Research Cat# D5002 ChamQ Universal SYBR qPCR Master Mix Vazyme Cat# Q711 Dynabeads mRNA DIRECT purification kit Thermo Fisher Scientific Cat# 61011 NEBNext Magnesium RNA Fragmentation Module NEB Cat# E6150S RNA Clean & Concentrator-5 kit Zymo Research Cat# R1016 Direct-zol RNA Microprep Kit Zymo Research Cat# R2060 Deposited data m6A-QTL summary statistics for brain, lung, muscle, and heart tissues from the eGTEx project Xiong et al.21 https://compbio.mit.edu/m6AQTLs/m6A. .. QTL.Xiong.etal/SumStat/ haQTL summary statistics for brain, lung, muscle, and heart tissues from the eGTEx project Hou et al.50 https://zenodo.org/records/7992724 mQTL summary statistics for lung and muscle tissues from the eGTEx project Oliva et al.51 https://gtexportal.org/home/datasets Code used in this study This manuscript https://doi.org/10.5281/zenodo.11481934 Experimental models: Cell lines Human: A549 ATCC(CRL-185) N/A Human: HEK293T ATCC(CRL-11268) N/A Oligonucleotides Oligonucleotides used in this study for experimental validation Table S13 N/A Recombinant DNA Plasmid: pLKO.1 Moffat et al.92 Addgene Plasmid # 10878 Plasmid: psPAX2 Trono Lab Packaging and Envelope Plasmids (unpublished) Addgene Plasmid # 12260 Plasmid: pMD2.G Trono Lab Packaging and Envelope Plasmids (unpublished) Addgene Plasmid # 12259 (Continued on next page) Cell Genomics 4, 100605, August 14, 2024 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms TwoSampleMR v0.5.6 Hemani et al.93 https://mrcieu.github.io/TwoSampleMR/ SMR Zhu et al.53 https://yanglab.westlake.edu.cn/software/ smr/ bedtools v2.31.0 Quinlan et al.94 https://bedtools.readthedocs.io/en/latest/ coloc v5.2.2 Giambartolomei et al.54 https://chr1swallace.github.io/coloc/ S-LDSC v1.0.1 Bulik-Sullivan et al.82 https://github.com/bulik/ldsc moloc v0.1.0 Giambartolomei et al.73 https://github.com/clagiamba/moloc Other Protein A/G Magnetic Beads Selleck Cat# B23201
other:Article Title: Prevention of transgene silencing during human pluripotent stem cell differentiation.
Article Snippet: In brief Stable transgene expression remains challenging during human pluripotent stem cell differentiation.. Wernig and colleagues show that combining CAG/ Ubc promoters with WPRE prevents transgene silencing following both random and targeted integration.. This work provides a broadly applicable genetic tool for studies requiring sustained transgene expression during differentiation of pluripotent stem cells.
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